Understanding not only what happens, but how much it matters

Coastal ecosystems are shaped by the movement of nutrients and organic matter from rivers, groundwater, and the open ocean, as well as by biological production and the activities of organisms themselves.

Our research asks:

What is happening? Why is it happening? And how important is it at the ecosystem scale?

We study these questions across a wide range of organisms, habitats, and spatial scales, with particular emphasis on biological production, material cycling, and the ecological processes that connect them.

Our goal is to quantify these processes and translate them into ecosystem-scale measures that can be compared and interpreted.

1. How strongly do organisms shape coastal ecosystems?

Organisms are not simply passive components of ecosystems. Through feeding, excretion, sediment disturbance, predation, and habitat modification, they can substantially alter material cycling and ecosystem structure.

Bivalves and material cycling

Bivalves provide a clear example of how population processes and ecosystem processes are connected.

Their growth, feeding, excretion, respiration, and mortality directly affect the movement of carbon and nutrients within coastal ecosystems.

In some of our studies, dense bivalve populations were found to exert feeding pressure far greater than local primary production, indicating that their influence extends well beyond the immediate area they occupy.

Other studies showed that bivalve mats can accumulate large amounts of nitrogen in surface sediments, demonstrating that organisms themselves can create important pathways of material retention and transformation.

How important is predation?

We also examine the effects of predators on coastal populations.

For example, we evaluated predation by ducks on Manila clams using field exclusion experiments, fixed cameras, and drone observations.

Rather than assuming that visible predation necessarily has a large population-level effect, we ask how much of the population is actually affected.

This kind of quantitative evaluation helps distinguish processes that are visually conspicuous from those that are truly important at the ecosystem or population scale.

Related publications

Selected publications on bivalves, material cycling, ecosystem engineering, and predator effects are listed here.

•  Honda, et al. (2025) Impact of duck predation on the population of Manila clam (Ruditapes philippinarum) in tidal flat. Estuarine, Coastal and Shelf Science, 109247, https://doi.org/10.1016/j.ecss.2025.109247

• Takenaka et al. (2018) Accumulation of organic matter within a muddy carpet created by the Asian date mussel, Arcuatula senhousia, on the Midori River tidal flats, Japan. Plankton and Benthos Research 13 (1), 1-9 

• Komorita, et al. (2014)  Food sources for Ruditapes philippinarum in a coastal lagoon determined by mass balance and stable isotope approaches. Plos one 9 (1), e86732 

•  Komorita, et al. (2010) Reevaluation of the nutrient mineralization process by infaunal bivalves (Ruditapes philippinarum) in a shallow lagoon in Hokkaido, Japan. Journal of Experimental Marine Biology and Ecology 383 (1), 8-16 

2. Measuring biological production in coastal ecosystems

Biomass tells us how much biological material is present.

Production tells us how fast that material is being created.

For understanding ecosystem function and material cycling, this distinction is essential.

Microphytobenthos

Microphytobenthos are major primary producers on tidal flats, but their production is highly variable in time and space.

We have worked to improve methods for estimating their primary production, including approaches that account for continuously changing light conditions rather than relying only on short-term incubations.

We also use multispectral drone imagery to extend point measurements of chlorophyll and primary producers across much larger areas of tidal flats.

From ecosystem structure to ecosystem function

We are also interested in how to evaluate ecological restoration.

In seaweed beds, restoration is often assessed using structural indicators such as area, cover, biomass, or species composition.

However, a restored habitat may look similar to a natural one while functioning differently.

We therefore use continuous dissolved oxygen observations to estimate ecosystem metabolism, including:

• Gross Primary Production (GPP)

• Ecosystem Respiration (ER)

• Net Ecosystem Production (NEP)

This allows us to evaluate not only whether a seaweed bed has returned, but also whether its ecological functions have recovered.

Related publications

• Ozaki, et al. (2025) Validation of the in situ slurry method for measuring primary production of microphytobenthos in tidal flats as compared to culture experiments and mooring systems.  Plankton & Benthos Research, 20, 194-204. https://doi.org/10.3800/pbr.20.194 

• Komorita, et al. (2016) Temporal variation in water intrusion of a tidal frontal system and distribution of chlorophyll in the Seto Inland Sea, Japan. Continental Shelf Research 112, 68-77

• Komorita,et al. (2012) Oceanic nutrient supply and uptake by microphytobenthos of the Hichirippu Lagoon, Hokkaido, Japan. Marine Ecology Progress Series 446, 161-171 

3. Where do materials come from, and how much do they support biological production?

Coastal biological production is supported by materials supplied from many sources.

These include:

• rivers

• groundwater

• sediments

• offshore waters

• internal regeneration within the ecosystem

A major focus of our research is to determine which sources are important, how much they contribute, and how efficiently those materials are used by organisms.

The influence of the Kuroshio

In Kagoshima Bay, we have studied how intrusions of Kuroshio-derived water affect nutrient supply and phytoplankton blooms.

Using shipboard observations and mixing models, we showed that offshore water intrusion can supply nutrients to the bay and support biological production.

We have also examined how phytoplankton and microzooplankton communities respond after these intrusion events.

More recently, satellite observations have allowed us to extend these studies from individual stations and transects to the scale of the entire bay.

By combining approximately 250-m-resolution satellite data with frequent ferry observations, we can examine how short-lived offshore water intrusions influence phytoplankton blooms over large spatial scales.

Related publications

Selected publications on Kuroshio intrusion, nutrient supply, plankton dynamics, and satellite observations are listed here.

• Komorita et al. (2021) Spring phytoplankton blooms in the Northern Satsunan region, Japan, stimulated by the intrusion of Kuroshio Branch water. Estuarine, Coastal and Shelf Science, 259, 107472

• Komorita et al. (2024) Temporal changes in the microplankton community due to Kuroshio branch current inflow. Regional Studies in Marine Science, 103576. https://doi.org/10.1016/j.rsma.2024.103576

• Komorita et al. Spatial Analysis of the Impact of Kuroshio Branch Intrusion on the Phytoplankton Bloom in Kagoshima Bay Using GCOM-C SGLI Data. Continental Shelf Research, in press.

4. Expanding our research toolkit to answer ecological questions

We do not define our research by a single method.

Instead, we have gradually expanded our toolkit as new questions have emerged.

Depending on the research question, we use:

• field observations of organisms, water, and sediments

• laboratory and field measurements of primary production

• stable isotope analysis

• radon and radium isotopes

• environmental DNA (eDNA)

• continuous environmental sensors

• fixed cameras

• drones

• satellite remote sensing

• statistical and spatial analysis

• machine learning

New technology is not the goal in itself.

We introduce or develop methods when they are needed to capture a process that could not otherwise be quantified.

For example, environmental DNA can provide information on fish distributions over large river systems, while drones can extend observations across entire tidal flats. Satellite data allow us to examine processes at the scale of bays, and machine learning can help estimate biological production continuously from environmental observations.

The method changes with the question.

The question comes first.

Current Research

Nutrient supply and biological production in the Yatsushiro Sea

We are currently investigating the nutrient budget of the Yatsushiro Sea.

Nutrients are supplied to the coastal sea from rivers, submarine groundwater discharge, sediments, and offshore waters.

However, the amount entering the coastal system is not necessarily the same as the amount ultimately available to phytoplankton in the water column.

One of our central questions is:

How much of the externally supplied nutrients actually reach and support pelagic biological production?

In particular, we are examining whether microphytobenthos on extensive tidal flats intercept and use nutrients before they reach the water column.

By combining nutrient budgets, groundwater tracers, tidal-flat primary production, continuous observations, and satellite data, we aim to quantify the role of tidal flats in regulating nutrient availability at the scale of the entire bay.

Red tides and primary production in the Yatsushiro Sea

We are also studying the production and nutrient requirements of harmful algal blooms.

During blooms of Karenia mikimotoi, we estimate primary production from environmental variables using machine-learning models and compare this production with the available nutrient stock and rates of nutrient regeneration.

This allows us to ask not only whether a bloom occurs, but also:

• how much production is taking place

• how rapidly nutrients are being consumed

• how long the available nutrient pool can sustain the bloom

By connecting bloom dynamics to nutrient budgets, we aim to understand the conditions that allow red tides to persist.

Seaweed-bed restoration and ecosystem function in Minamata

Along the coast of Minamata, we are evaluating the recovery of seaweed beds from both structural and functional perspectives.

We combine observations of seaweed distribution and biomass with continuous dissolved oxygen measurements to estimate ecosystem metabolism.

This allows us to determine whether restoration has recovered not only the appearance of a seaweed bed, but also its capacity for primary production and ecosystem-level metabolism.

Connecting dams, rivers, estuaries, and the sea through ecological restoration

Sediment movement connects entire watersheds.

Sediment trapped behind dams can alter downstream river habitats, migration pathways, estuaries, and tidal flats.

We are studying how the strategic placement and movement of sediment can contribute to ecological restoration from rivers to coastal environments.

Current work includes:

• improving migration pathways for aquatic organisms

• evaluating fish distribution using environmental DNA

• examining effects on aquatic insects and benthic communities

• increasing habitat diversity downstream

• restoring tidal-flat environments for bivalves

Rather than treating dams, rivers, and coastal areas as separate systems, we aim to understand them as an interconnected ecological network.

How strongly do animals physically modify tidal flats?

Animals can physically transform their environments.

We are currently quantifying sediment disturbance caused by fish on tidal flats.

By combining environmental DNA, drone observations, and direct field measurements, we estimate which fish are responsible for disturbance and how much of the tidal-flat surface is modified over time.

The key question is not simply whether fish disturb the sediment, but:

What proportion of the tidal flat do they actually modify?

Quantifying this process at the ecosystem scale allows us to evaluate whether animal-driven sediment disturbance should be considered a major component of tidal-flat ecosystem dynamics.

Linking offshore oceanographic processes to coastal biological production

Our work on Kuroshio intrusions continues to expand.

By combining shipboard observations, ferry measurements, continuous monitoring, and satellite remote sensing, we investigate how offshore oceanographic processes influence nutrient supply and biological production in coastal seas.

This work helps connect processes that are often studied separately: open-ocean circulation and coastal ecosystem dynamics.

What We Aim to Understand

Our research covers a wide range of organisms and environments, including bivalves, microphytobenthos, phytoplankton, seaweeds, fish, birds, red tides, groundwater, rivers, tidal flats, bays, and offshore waters.

Our field sites and methods also vary widely.

But the questions that guide our research are consistent:

What is happening?
Why is it happening?
How important is it at the ecosystem scale?

We quantify ecological processes because the numbers themselves are not the final goal.

By comparing the magnitude of different processes, we can identify which processes truly support ecosystem function, which environmental changes matter most, and which factors deserve priority in conservation and restoration.

Ultimately, we aim to build a quantitative understanding of coastal ecosystems that can contribute to their conservation, restoration, and sustainable use.